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Wednesday, July 08, 2009

JChemPaint-Primary moving to Git

I knew it was going to be painful, but making the jchempaint-primary branch a proper patch to the CDK master branch is painful. I am working my way towards setting up a git repository (IMPORTANT: these patches are not final yet, and their history will change, as I am rebasing regularly to make cleaner patches! Making copies is save, but please hold of any forking and/or branching on top of it until it is final. Thanx.) for the patch, with split ups of the various parts into reviewable blobs:

As you can see (when you click on the image to enlarge it), I have more or less finished the first drafts of the patch sets (see this wiki page) 0-other, 1-render, 2-renderbasic, 9-rendercontrol, and 6-control. The last one does not actually compile properly yet, as I need to abstract an IRenderer interface first.

There are several patch sets that I am still porting, but I hope to finish that this week, after which I'll continue working on the new IEdit framework in the controller modules recently set up by Arvid.

It will take some time before these patches actually get submitted for review, as there is quite some PMD, DocCheck and unit testing work to be done, as is clear from the Nightly running on the SVN branch.

Finally, I like to note that this git repository collapses a lot of work done by developers at both Uppsala University (Arvid, Ola and me) and the EBI (Gilleain, Stefan and now Mark). While the above git history will not reflect those contributions, you can recover this information from the copyright headers. I also like to thank Lars and Sam for their valuable testing!

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

About Me

Assistant professor at the Dept of Bioinformatics - BiGCaT at NUTRIM, Maastricht University, studying biology at an unsupervised and atomic level. Open Science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and WikiPathways. ORCID:0000-0001-7542-0286. Posts on G+ are personal.

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